Polygenic Score (PGS) ID: PGS001898

Predicted Trait
Reported Trait Ever depressed for a whole week
Mapped Trait(s) depressive symptom measurement (EFO_0007006)
Additional Trait Information psychiatric disorders
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_depressed_for_1w
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 5,777
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
391,124 individuals European UK (+ Ireland) UKB

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM010067 PSS009394|
European Ancestry|
6,445 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever depressed for a whole week Partial Correlation (partial-r): 0.0769 [0.0526, 0.1012] sex, age, birth date, deprivation index, 16 PCs
PPM010068 PSS009168|
European Ancestry|
1,519 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever depressed for a whole week Partial Correlation (partial-r): -0.0019 [-0.0525, 0.0488] sex, age, birth date, deprivation index, 16 PCs
PPM010069 PSS008722|
European Ancestry|
2,506 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever depressed for a whole week Partial Correlation (partial-r): 0.0432 [0.0039, 0.0824] sex, age, birth date, deprivation index, 16 PCs
PPM010070 PSS008496|
Greater Middle Eastern Ancestry|
505 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever depressed for a whole week Partial Correlation (partial-r): 0.0058 [-0.0833, 0.0947] sex, age, birth date, deprivation index, 16 PCs
PPM010072 PSS008051|
East Asian Ancestry|
751 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever depressed for a whole week Partial Correlation (partial-r): -0.028 [-0.1003, 0.0446] sex, age, birth date, deprivation index, 16 PCs
PPM010073 PSS007838|
African Ancestry|
1,457 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever depressed for a whole week Partial Correlation (partial-r): 0.0344 [-0.0173, 0.086] sex, age, birth date, deprivation index, 16 PCs
PPM010074 PSS008942|
African Ancestry|
2,067 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever depressed for a whole week Partial Correlation (partial-r): -0.031 [-0.0742, 0.0123] sex, age, birth date, deprivation index, 16 PCs
PPM010071 PSS008274|
South Asian Ancestry|
3,525 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever depressed for a whole week Partial Correlation (partial-r): 0.026 [-0.0071, 0.0591] sex, age, birth date, deprivation index, 16 PCs

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS008942 2,067 individuals African unspecified Nigeria (West Africa) UKB
PSS008496 505 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009168 1,519 individuals European Poland (NE Europe) UKB
PSS008722 2,506 individuals European Italy (South Europe) UKB
PSS009394 6,445 individuals European UK (+ Ireland) UKB
PSS008051 751 individuals East Asian China (East Asia) UKB
PSS008274 3,525 individuals South Asian India (South Asia) UKB
PSS007838 1,457 individuals African American or Afro-Caribbean Carribean UKB